Optimizing integration of scRNA-seq and scATAC-seq datasets

/PBMC_benchmark/ comparison of integration methods on PBMC dataset from 10X genomics
- 20191111_fracQuery_EDA.Rmd contains method run time and robustness analysis
- 20191111_labelTransferEDA_PBMC.Rmd contains comparison of label transfer outcomes (visualization, prediction score analysis, KNN purity analysis)
- 20191113_clusterSize_PBMC.Rmd contains comparison of dependency of label transfer on cluster size
/Thymus_benchmark/ comparison of integration methods and featurizarion strategies on Fetal thymus dataset
- *_labelTransferEDA_thymus_v2* contain comparison of label transfer outcomes (visualization, prediction score analysis, KNN purity analysis), w different featurization strategy (binary gmat/counts gmat) and feature selection methods (joint/reference-based)
- 20191125_gmat_EDA.Rmd exploration of featurization strategies outcomes on scATAC-seq data
/Tcell_maturation_analysis/ integrative analysis of T cell trajectory in fetal thymus
/preprocess/ scripts/notebooks for preprocessing and explorative data analysis of scRNA-seq and scATAC-seq datasets
/report/ bookdown project for final report
/run_integration_wrappers/ wrappers to run workflow for method comparison
/scIntegrationBM/ R package for bechmarking of integration methods (work in progress)
/test_methods/ scripts for reproducing vignettes of integration methods
/thrashNsnippets/ misc

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Comparison of multi-omic integration methods for single-cell data.

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